WGCNA - clustering RNA expression

Question

[eilalandkof]

Hello,

I am using WGCNA to cluster RNA expression data. I have the reads and the RPKM data available dim(expressionRPKMClean) [1] 25755 972

i have 972 cell lines and 25,755 cell lines expression.

the clustering identify one small cluster. the remainder is greyed.

Any idea what might be the issue. I can post code as well

Thanks, Eila

[Lluís R.]

The more homogeneous the better for module finding. Are you sure you have 972 different cell lines instead of samples? The 25,755 seems to be different RNA-seq. Did you check in a PCA or MDS or similar techniques how similar are the samples? How did you identify your modules? Did you use goodSamplesGenes in the data set to check the variance of the samples and of the RNA?